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Samardak K, Bâcle J, Moriel-Carretero M. Behind the stoNE wall: A fervent activity for nuclear lipids. Biochimie 2024:S0300-9084(24)00179-2. [PMID: 39111564 DOI: 10.1016/j.biochi.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/27/2024]
Abstract
The four main types of biomolecules are nucleic acids, proteins, carbohydrates and lipids. The knowledge about their respective interactions is as important as the individual understanding of each of them. However, while, for example, the interaction of proteins with the other three groups is extensively studied, that of nucleic acids and lipids is, in comparison, very poorly explored. An iconic paradigm of physical (and likely functional) proximity between DNA and lipids is the case of the genomic DNA in eukaryotes: enclosed within the nucleus by two concentric lipid bilayers, the wealth of implications of this interaction, for example in genome stability, remains underassessed. Nuclear lipid-related phenotypes have been observed for 50 years, yet in most cases kept as mere anecdotical descriptions. In this review, we will bring together the evidence connecting lipids with both the nuclear envelope and the nucleoplasm, and will make critical analyses of these descriptions. Our exploration establishes a scenario in which lipids irrefutably play a role in nuclear homeostasis.
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Affiliation(s)
- Kseniya Samardak
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France.
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2
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Penzo A, Palancade B. Puzzling out nuclear pore complex assembly. FEBS Lett 2023; 597:2705-2727. [PMID: 37548888 DOI: 10.1002/1873-3468.14713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Nuclear pore complexes (NPCs) are sophisticated multiprotein assemblies embedded within the nuclear envelope and controlling the exchanges of molecules between the cytoplasm and the nucleus. In this review, we summarize the mechanisms by which these elaborate complexes are built from their subunits, the nucleoporins, based on our ever-growing knowledge of NPC structural organization and on the recent identification of additional features of this process. We present the constraints faced during the production of nucleoporins, their gathering into oligomeric complexes, and the formation of NPCs within nuclear envelopes, and review the cellular strategies at play, from co-translational assembly to the enrolment of a panel of cofactors. Remarkably, the study of NPCs can inform our perception of the biogenesis of multiprotein complexes in general - and vice versa.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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3
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Veldsink AC, Gallardo P, Lusk CP, Veenhoff LM. Changing the guard-nuclear pore complex quality control. FEBS Lett 2023; 597:2739-2749. [PMID: 37715940 DOI: 10.1002/1873-3468.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/18/2023]
Abstract
The integrity of the nuclear envelope depends on the function of nuclear pore complexes (NPCs), transport channels that control macromolecular traffic between the nucleus and cytosol. The central importance of NPCs suggests the existence of quality control (QC) mechanisms that oversee their assembly and function. In this perspective, we emphasize the challenges associated with NPC assembly and the need for QC mechanisms that operate at various stages of an NPC's life. This includes cytosolic preassembly QC that helps enforce key nucleoporin-nucleoporin interactions and their ultimate stoichiometry in the NPC in addition to mechanisms that monitor aberrant fusion of the inner and outer nuclear membranes. Furthermore, we discuss whether and how these QC mechanisms may operate to sense faulty mature NPCs to facilitate their repair or removal. The so far uncovered mechanisms for NPC QC provide fertile ground for future research that not only benefits a better understanding of the vital role that NPCs play in cellular physiology but also how loss of NPC function and/or these QC mechanisms might be an input to aging and disease.
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Affiliation(s)
- Annemiek C Veldsink
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, CT, New Haven, USA
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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4
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [PMID: 37974978 PMCID: PMC10643749 DOI: 10.1007/s12551-023-01136-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 11/19/2023] Open
Abstract
Nuclear cytoplasmic transport is mediated by many receptors that recognize specific nuclear localization signals on proteins and RNA and transport these substrates through nuclear pore complexes. Facilitated diffusion through nuclear pore complexes requires the attachment of transport receptors. Despite the relatively large tunnel diameter, some even small proteins (less than 20-30 kDa), such as histones, pass through the nuclear pore complex only with transport receptors. Over several decades, considerable material has been accumulated on the structure, architecture, and amino acid composition of the proteins included in this complex and the sequence of many receptors. We consider the data available in the literature on the structure of the nuclear pore complex and possible mechanisms of nuclear-cytoplasmic transport, applying the theory of electrostatic interactions in the context of our data on changes in the electrokinetic potential of nuclei and our previously proposed physical model of the mechanism of facilitated diffusion through the nuclear pore complex (NPC). According to our data, the main contribution to the charge of the nuclear membrane is made by anionic phospholipids, which are part of both the nuclear membrane and the nuclear matrix, which creates a potential difference between them. The nuclear membrane is a four-layer phospholipid dielectric, so the potential vector can only pass through the NPC, creating an electrostatic funnel that "pulls in" the positively charged load-NLS-NTR trigger complexes. Considering the newly obtained data, an improved model of the previously proposed physical model of the mechanism of nuclear-cytoplasmic transport is proposed. This model considers the contribution of electrostatic fields to the transportation speed when changing the membrane's thickness in the NPC basket at a higher load.
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Affiliation(s)
- Liya A. Minasbekyan
- Scientific Research Institute of Biology, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
| | - Hamlet G. Badalyan
- Chair of General Physics, Yerevan State University, A. Manoogian St., 1, 0025 Yerevan, Armenia
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5
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Kuiper EFE, Prophet SM, Schlieker C. Coordinating nucleoporin condensation and nuclear pore complex assembly. FEBS Lett 2023; 597:2534-2545. [PMID: 37620293 DOI: 10.1002/1873-3468.14725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
The nuclear pore complex (NPC) is among the most elaborate protein complexes in eukaryotes. While ribosomes and proteasomes are known to require dedicated assembly machinery, our understanding of NPC assembly is at a relatively early stage. Defects in NPC assembly or homeostasis are tied to movement disorders, including dystonia and amyotrophic lateral sclerosis (ALS), as well as aging, requiring a better understanding of these processes to enable therapeutic intervention. Here, we discuss recent progress in the understanding of NPC assembly and highlight how related defects in human disorders can shed light on NPC biogenesis. We propose that the condensation of phenylalanine-glycine repeat nucleoporins needs to be carefully controlled during NPC assembly to prevent aberrant condensation, aggregation, or amyloid formation.
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Affiliation(s)
- E F Elsiena Kuiper
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Sarah M Prophet
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
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6
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Minasbekyan LA, Badalyan HG. Physical model of the nuclear membrane permeability mechanism. Biophys Rev 2023; 15:1195-1207. [DOI: https:/doi.org/10.1007/s12551-023-01136-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/31/2023] [Indexed: 02/27/2024] Open
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7
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Amm I, Weberruss M, Hellwig A, Schwarz J, Tatarek-Nossol M, Lüchtenborg C, Kallas M, Brügger B, Hurt E, Antonin W. Distinct domains in Ndc1 mediate its interaction with the Nup84 complex and the nuclear membrane. J Cell Biol 2023; 222:e202210059. [PMID: 37154843 PMCID: PMC10165475 DOI: 10.1083/jcb.202210059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/31/2023] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from ∼30 different nucleoporins (Nups) in multiple copies, few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1's transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1's C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1's amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.
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Affiliation(s)
- Ingo Amm
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
| | - Johannes Schwarz
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Martina Kallas
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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8
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Kralt A, Wojtynek M, Fischer JS, Agote-Aran A, Mancini R, Dultz E, Noor E, Uliana F, Tatarek-Nossol M, Antonin W, Onischenko E, Medalia O, Weis K. An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae. eLife 2022; 11:78385. [PMID: 36000978 PMCID: PMC9402233 DOI: 10.7554/elife.78385] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 12/28/2022] Open
Abstract
The nuclear pore complex (NPC) is the central portal for macromolecular exchange between the nucleus and cytoplasm. In all eukaryotes, NPCs assemble into an intact nuclear envelope (NE) during interphase, but the process of NPC biogenesis remains poorly characterized. Furthermore, little is known about how NPC assembly leads to the fusion of the outer and inner NE, and no factors have been identified that could trigger this event. Here, we characterize the transmembrane protein Brl1 as an NPC assembly factor required for NE fusion in budding yeast. Brl1 preferentially associates with NPC assembly intermediates and its depletion halts NPC biogenesis, leading to NE herniations that contain inner and outer ring nucleoporins but lack the cytoplasmic export platform. Furthermore, we identify an essential amphipathic helix in the luminal domain of Brl1 that mediates interactions with lipid bilayers. Mutations in this amphipathic helix lead to NPC assembly defects, and cryo-electron tomography analyses reveal multilayered herniations of the inner nuclear membrane with NPC-like structures at the neck, indicating a failure in NE fusion. Taken together, our results identify a role for Brl1 in NPC assembly and suggest a function of its amphipathic helix in mediating the fusion of the inner and outer nuclear membranes.
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Affiliation(s)
- Annemarie Kralt
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Jonas S Fischer
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Arantxa Agote-Aran
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Roberta Mancini
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Evgeny Onischenko
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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9
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Dultz E, Wojtynek M, Medalia O, Onischenko E. The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells 2022; 11:1456. [PMID: 35563762 PMCID: PMC9100368 DOI: 10.3390/cells11091456] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/01/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the only transport channels that cross the nuclear envelope. Constructed from ~500-1000 nucleoporin proteins each, they are among the largest macromolecular assemblies in eukaryotic cells. Thanks to advances in structural analysis approaches, the construction principles and architecture of the NPC have recently been revealed at submolecular resolution. Although the overall structure and inventory of nucleoporins are conserved, NPCs exhibit significant compositional and functional plasticity even within single cells and surprising variability in their assembly pathways. Once assembled, NPCs remain seemingly unexchangeable in post-mitotic cells. There are a number of as yet unresolved questions about how the versatility of NPC assembly and composition is established, how cells monitor the functional state of NPCs or how they could be renewed. Here, we review current progress in our understanding of the key aspects of NPC architecture and lifecycle.
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Affiliation(s)
- Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETHZ Zurich, 8093 Zurich, Switzerland;
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, ETHZ Zurich, 8093 Zurich, Switzerland;
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Evgeny Onischenko
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway
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10
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Vitale J, Khan A, Neuner A, Schiebel E. A perinuclear α-helix with amphipathic features in Brl1 promotes NPC assembly. Mol Biol Cell 2022; 33:ar35. [PMID: 35293775 PMCID: PMC9282021 DOI: 10.1091/mbc.e21-12-0616] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
How nuclear pore complexes (NPC) assemble in the intact nuclear envelope (NE) is only rudimentarily understood. Nucleoporins accumulate at the inner NE (INM), deform this membrane towards the outer nuclear membrane (ONM) and eventually INM and ONM fuse by an unclear mechanism. In budding yeast, the integral membrane protein Brl1 that transiently associates with NPC assembly intermediates is involved in INM/ONM fusion during NPC assembly but leaving the molecular mechanism open. AlphaFold predictions indicate that Brl1-like proteins carry as common motifs an α-helix with amphipathic features (AαH) and a disulfide-stabilized anti-parallel helix bundle (DAH) in the perinuclear space. Mutants with defective AαH (brl1F391E, brl1F391P, brl1L402E) impair the essential function of BRL1. Overexpression of brl1F391E promotes formation of INM and ONM enclosed petal-like structures that carry nucleoporins at their base suggesting that they are derived from an NPC assembly attempt with failed INM/ONM fusion. Accordingly, brl1F391E expression triggers mis-localisation of Nup159 and Nup42 and to a lesser extent Nsp1 that localize on the cytoplasmic face of the NPC. The DAH also contributes to the function of Brl1 and AαH has functions independent of DAH. We propose that AαH and DAH in Brl1 promote INM/ONM fusion during NPC assembly.
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Affiliation(s)
- Jlenia Vitale
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, 69120 Heidelberg, Germany
| | - Azqa Khan
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, 69120 Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany
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11
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Hamed M, Antonin W. Dunking into the Lipid Bilayer: How Direct Membrane Binding of Nucleoporins Can Contribute to Nuclear Pore Complex Structure and Assembly. Cells 2021; 10:3601. [PMID: 34944108 PMCID: PMC8700311 DOI: 10.3390/cells10123601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 02/07/2023] Open
Abstract
Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins are an integral part of NPCs and thought to anchor these complexes in the nuclear envelope. In addition, a number of nucleoporins without membrane spanning domains interact with the pore membrane. Here we review our current knowledge of how these proteins interact with the membrane and how this interaction can contribute to NPC assembly, stability and function as well as shaping of the pore membrane.
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Affiliation(s)
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany;
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